Result

Search results for the GEO ID: GSE13552

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GSM ID

GPL ID

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Title

Source name

Description

Characteristics

GSM341440

GPL1261

Jhdm2a wild-type skeletal muscle expression

wild-type skeletal muscle

Strain: 129 ES cell backcrossed onto C57BL/6 for 4 generations Gender: Male Age: 3 months Tissue: Skeletal muscle

None

Sample_geo_accession	GSM341440
Sample_status	Public on Feb 05 2009
Sample_submission_date	Nov 10 2008
Sample_last_update_date	Feb 05 2009
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Qiagen RNeasy Kit by manufacturers protocol (RNeasy mini protocol for isolation of total RNA from heart, muscle, and skin tissue).
Sample_label_ch1	biotin
Sample_label_protocol_ch1	7 ug of total RNA was used to synthesize cDNA. A custom cDNA kit from Life Technologies was used with a T7-(dT)24 primer for this reaction. Biotinylated cRNA was then generated from the cDNA reaction using the BioArray High Yield RNA Transcript Kit. The cRNA was then fragmented in fragmentation buffer (5X fragmentation buffer: 200mM Tris-acetate, pH8.1, 500mM KOAc, 150mM MgOAc) at 94oC for 35 minutes before the chip hybridization. 15 ug of fragmented cRNA was then added to a hybridization cocktail (0.05 ug/ul fragmented cRNA, 50 pM control oligonucleotide B2, BioB, BioC, BioD, and cre hybridization controls, 0.1 mg/ml herring sperm DNA, 0.5 mg/ml acetylated BSA, 100mM MES, 1M [Na+], 20mM EDTA, 0.01% Tween 20).
Sample_hyb_protocol	10 ug of cRNA was used for hybridization. Arrays were hybridized for 16 hours at 45oC in the GeneChip Hybridization Oven 640. The arrays were washed and stained with R-phycoerythrin streptavidin in the GeneChip Fluidics Station 400.
Sample_scan_protocol	the arrays were scanned with the Hewlett Packard GeneArray Scanner. Affymetrix GeneChip Microarray Suite 5.0 software was used for washing, scanning, and basic analysis. Sample quality was assessed by examination of 3’ to 5’ intensity ratios of certain genes.
Sample_data_processing	MAS5 algorithm was used for data generation.
Sample_platform_id	GPL1261
Sample_contact_name	Eric,M.,Kallin
Sample_contact_email	eric.kallin@crg.es
Sample_contact_laboratory	Thomas Graf
Sample_contact_department	Differentiation and Cancer
Sample_contact_institute	Center for Genomic Regulation
Sample_contact_address	C/ Dr. Aiguader, 88
Sample_contact_city	Barcelona
Sample_contact_state	Barcelona
Sample_contact_zip/postal_code	08003
Sample_contact_country	Spain
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM341nnn/GSM341440/suppl/GSM341440.CEL.gz
Sample_series_id	GSE13552
Sample_data_row_count	45101

GSM341441

GPL1261

Jhdm2a null skeletal muscle expression

Jhdm2a null skeletal muscle

Strain: 129 ES cell backcrossed onto C57BL/6 for 4 generations Gender: Male Age: 3 months Tissue: Skeletal muscle

None

Sample_geo_accession	GSM341441
Sample_status	Public on Feb 05 2009
Sample_submission_date	Nov 10 2008
Sample_last_update_date	Feb 05 2009
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Qiagen RNeasy Kit by manufacturers protocol (RNeasy mini protocol for isolation of total RNA from heart, muscle, and skin tissue).
Sample_label_ch1	biotin
Sample_label_protocol_ch1	7 ug of total RNA was used to synthesize cDNA. A custom cDNA kit from Life Technologies was used with a T7-(dT)24 primer for this reaction. Biotinylated cRNA was then generated from the cDNA reaction using the BioArray High Yield RNA Transcript Kit. The cRNA was then fragmented in fragmentation buffer (5X fragmentation buffer: 200mM Tris-acetate, pH8.1, 500mM KOAc, 150mM MgOAc) at 94oC for 35 minutes before the chip hybridization. 15 ug of fragmented cRNA was then added to a hybridization cocktail (0.05 ug/ul fragmented cRNA, 50 pM control oligonucleotide B2, BioB, BioC, BioD, and cre hybridization controls, 0.1 mg/ml herring sperm DNA, 0.5 mg/ml acetylated BSA, 100mM MES, 1M [Na+], 20mM EDTA, 0.01% Tween 20).
Sample_hyb_protocol	10 ug of cRNA was used for hybridization. Arrays were hybridized for 16 hours at 45oC in the GeneChip Hybridization Oven 640. The arrays were washed and stained with R-phycoerythrin streptavidin in the GeneChip Fluidics Station 400.
Sample_scan_protocol	the arrays were scanned with the Hewlett Packard GeneArray Scanner. Affymetrix GeneChip Microarray Suite 5.0 software was used for washing, scanning, and basic analysis. Sample quality was assessed by examination of 3’ to 5’ intensity ratios of certain genes.
Sample_data_processing	MAS5 algorithm was used for data generation.
Sample_platform_id	GPL1261
Sample_contact_name	Eric,M.,Kallin
Sample_contact_email	eric.kallin@crg.es
Sample_contact_laboratory	Thomas Graf
Sample_contact_department	Differentiation and Cancer
Sample_contact_institute	Center for Genomic Regulation
Sample_contact_address	C/ Dr. Aiguader, 88
Sample_contact_city	Barcelona
Sample_contact_state	Barcelona
Sample_contact_zip/postal_code	08003
Sample_contact_country	Spain
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM341nnn/GSM341441/suppl/GSM341441.CEL.gz
Sample_series_id	GSE13552
Sample_data_row_count	45101

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